Introduction to Data Analysis

in Microbial Ecology

Introduction to Bioinformatics

Bioinformatics applies computational methods to store, manage, and analyse biological data

• Experiments involving sequencing generates too much data to analyse manually
• Your Nanopore sequencing generated ~ 100,000 sequencing reads
• Computational tools allow you to store, filter and analyse such data

The Command Line Interface (CLI)

A text-based interface for giving instructions to a computer

High Performance Computing (HPC)

A shared computer system that provides more memory, CPUs, space than a typical laptop

Real-life application

In this tutorial, you will analyse these reads to:

• Determine which strains are present in the mixed communities
• Quantify their relative abundances
• Asses whether the counts fit with your assumptions about individual interactions

Workflow

flowchart TB
    classDef greenfill fill:#5B888C,stroke:#333,stroke-width:1,color:#fff;
    classDef dbfill fill:#E2F0F1,stroke:#333,stroke-width:1,color:#333;

    %% Reference database node
    DB[(16S <br> Reference  <br> Database)] ---->|FASTA| D  

    %% Workflow boxes
    A[Raw reads] -->|FASTQ| B[Quality control]
    B -->|FASTQ| C[Quality filtering]
    C -->|FASTQ| D[Alignment to <br> Reference DB]
    D -->|PAF| E[Count table]

    %% Assign classes after nodes exist
    class A,B,C,D,E greenfill
    class DB dbfill

    %% Arrow styles (index starts at 0 for first arrow)
    linkStyle 0,1,2,3,4 stroke:#5B888C,stroke-width:2,color:#000, fill: none

Practical part

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